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- #Change nuclotide contig in bioedit how to
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These analyses indicated that gene content was highly conserved between G19833 and OAC-Rex across the regions examined (>80%). vulgaris-derived CBB-resistance on chromosome 10, were compared.
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In addition, the genomic regions containing SAP6, a marker associated with P. vulgaris line G19833, which is a large seeded bean of Andean origin, and (assumed to be) CBB susceptible. Our current whole genome sequencing effort with OAC-Rex provided the opportunity to compare its genome in the regions associated with CBB resistance with the v1.0 release of the P. Resistance to CBB is assumed to be derived from an interspecific cross with Phaseolus acutifolius in the pedigree of OAC-Rex. Previous studies with OAC-Rex, a CBB-resistant, white bean variety of Mesoamerican origin, identified two resistance loci associated with the molecular markers Pv-CTT001 and SU91, on chromosome 4 and 8, respectively.
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phaseoli, in Phaseolus vulgaris is conditioned by several loci on different chromosomes. Resistance to common bacterial blight, caused by Xanthomonas axonopodis pv. 4Greenhouse and Processing Crops Research Centre, Agriculture and Agri-Food Canada, Harrow, ON, Canada.3Agriculture and Agri-Food Canada, c/o Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada.2Department of Biological Sciences, University of Windsor, Windsor, ON, Canada.1Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada.
#Change nuclotide contig in bioedit install
If you don’t yet, then definitely consider running through the Unix crash course first ?įor a while, this was also kind of a huge pain to install on some systems.Gregory Perry 1*, Claudia DiNatale 2, Weilong Xie 3, Alireza Navabi 3, Yarmilla Reinprecht 1, William Crosby 2, Kangfu Yu 4, Chun Shi 4 and K. This page assumes you already have some familiarity with working at the command line. NOTE: This stuff can look messy, mostly because it is it scares me too.
#Change nuclotide contig in bioedit archive
This page holds some of the ways I’ve used EDirect, both to serve as a handy archive for myself, and to hopefully help others ? It won’t be as comprehensive as most other things on this site, as it’s extremely expansive and it’s still nowhere near intuitive for me ?♂️ But these examples may do what is needed, and if not they at least might provide good starting points for building the code that will do what is needed. And I often end up digging through several of my old log files to find things, so… But I still have trouble finding examples when I need them (and I always need them when using this).
#Change nuclotide contig in bioedit trial
Those are where I’ve learned from (along with a lot of trial and error). There is a lot of info on this at the main NCBI EDirect page, and some more here.
#Change nuclotide contig in bioedit download
But like a lot of things, once I had a little familiarity with it, I started to appreciate how useful and powerful it can be.īeing able to access data and info from NCBI at the command line can allow us to: automate and document things well (we can give the exact command used to retrieve information and the date it was executed, rather than “pulled from NCBI”) download directly to a server rather than our local computer pull more specific information than we can on the site and more ? Learning to use it at all was painful at times for me – and still is when I’m trying to figure out new stuff with it. EDirect is a set of tools NCBI provides to enable accessing the vast amount of information stored at NCBI from the command line. I also put together a small program specifically for downloading assemblies by accession when making GToTree, and I found it useful in general so it’s also now part of my Bioinf Tools as bit-dl-ncbi-assemblies.īut there have been times when I needed more than these could offer, which required me spending a decent amount of time getting used to using NCBI’sĮDirect tools. For searching by taxonomy and downloading genomes (assemblies), and some others have put together a great tool called ncbi-genome-download, and they have one for downloading individual sequences by accession called ncbi-acc-download. There are some convenient tools available that may help in some situations depending on our needs.
#Change nuclotide contig in bioedit how to
But sometimes it can be a little tricky to figure out how to download the data we want – particularly when it’s a lot of things and we want and/or need to do it at the command-line rather than at the site.